There's a bit where the bitchy one with the clot is on the radio and everyone looks to her, leaving the 2 doctors alone. Conceivable when the swap happened.

As for the fake-Amy execution, I agree, it seemed really harsh. Maybe next week it'll be a "I had to kill her,staying connected would harm the baby." or something.Bear in mind that it wasn't a separate Amy like the other gangers, it was just normal Amy piloting a flesh clone. She didn't die, so much as snap back to her real body.